#if !defined(GENES_SANS_ORPHANS_H)
#define GENES_SANS_ORPHANS_H
#include <vector>
#include <deque>

//
//	Use coordinates after orphans are removed
//
void get_gene_pos_sans_orphans(	const std::deque<std::deque<unsigned> >		gene_pos_by_chromosome[],
								std::vector<unsigned>&						gene_pos_to_rel_gene_pos,
								std::deque<unsigned>&						rel_gene_pos_to_gene_pos,
								const std::deque<std::deque<unsigned> >&	ortholog_sets,
								std::deque<std::deque<unsigned> >&			rel_ortholog_sets,
								std::vector<char>&							gene_pos_to_orphan,
								const std::vector<signed char>&				gene_pos_to_strand,
								std::vector<signed char>&					rel_gene_pos_to_strand);

#endif

